[gmx-users] problem: gromacs run on gpu

Szilárd Páll pall.szilard at gmail.com
Sat Jul 8 15:43:04 CEST 2017


If you want to use only one GPU, pass that GPU's ID to mdrun, e.g. -gpu_id
0 for the 1st one. You'll also want to pick the right number of cores for
the run, it will surely not make sense to use all 96. Also make sure to pin
the threads (-pin on).

However, I strongly recommend that you read the documentation and wiki and
check the examples to understand how to correctly launch mdrun and how to
understand performance and tune it. You should especially be careful if you
intend to share the node with others or you want to do multiple runs


On Fri, Jul 7, 2017 at 10:55 PM, leila karami <karami.leila1 at gmail.com>

> *Dear Nikhil and Szilárd,*
> Thanks for your answers.
> I want to use only one of GPUs (for example ID =1).
> Should I use option -gpu_id 1?
> Information of my system hardware is as follows:
> Running on 1 node with total 96 cores, 192 logical cores, 3 compatible GPUs
> Hardware detected on host cschpc.ut.ac.ir (the node of MPI rank 0).
> Since there is 1 node in my system, should I use both of -ntmpi and
> -ntomp or just -ntomp?
> Should I obtain optimum values for -ntmpi and -ntomp using trial and
> error? Is not there another way?
> Best wishes.
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